|
| Status |
Public on Nov 03, 2021 |
| Title |
WT_RNAseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LSK Cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
cell type: LSK Cells
|
| Growth protocol |
Lin- bone marrow cells were enriched using the Direct Lineage Cell Depletion kit with LS columns (Miltenyi Biotec). Enriched Lin- cells were stained with the mouse bone marrow biotin lineage panel, Streptavidin APC- cy7, APC-c-Kit and PEcy7-Sca-1, and after staining all HSPCs were sorted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 1- 2x105 sorted HSPCs using AllPrep DNA/RNA Plus micro kit (Qiagen). Ribosomal RNA was removed using the NEBNext rRNA Depletion kit (New England Biolabs #E6310) following manufacturer’s instructions.
RNA-Seq libraries were prepared using the Universal Plus mRNA-Seq kit (NuGEN Technologies).
Paired-End, 100bp sequenced on an Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RSEM.count.matrix.txt
|
| Data processing |
Base calling using Illumina RTA 2.4.11
Reads were aligned to the mm10 transcriptome and ERCC spike-in indicies using RSEM (v1.3.0) and STAR (v2.6.0c) with Gencode annotations.
Genome_build: Encode: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Excel file contains aggregated RSEM gene.results output with expected counts for all samples.
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Stephen Nimer |
| Organization name |
University of Miami
|
| Department |
Sylvester Comprehensive Cancer Center
|
| Street address |
1120 NW 14th ST
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE145819 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [RNA-Seq] |
| GSE145878 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN14171973 |
| SRA |
SRX7792241 |
